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Various bug fixes

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This commit is contained in:
Landon Wark
2024-03-07 14:26:29 -06:00
parent b466cb61d2
commit d0418ebc9e
7 changed files with 80 additions and 37 deletions
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33
src/submissions/backend/db/models/submissions.py
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@@ -9,7 +9,7 @@ from tempfile import TemporaryDirectory
from reportlab.graphics.barcode import createBarcodeImageInMemory
from reportlab.graphics.shapes import Drawing
from reportlab.lib.units import mm
from operator import attrgetter
from operator import attrgetter, itemgetter
from pprint import pformat
from . import Reagent, SubmissionType, KitType, Organization
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
@@ -1349,11 +1349,13 @@ class WastewaterArtic(BasicSubmission):
Returns:
dict: Updated sample dictionary
"""
from backend.validators import RSLNamer
input_dict = super().parse_info(input_dict)
df = xl.parse("First Strand List", header=None)
plates = []
for row in [8,9,10]:
plates.append(dict(plate=df.iat[row-1, 2], start_sample=df.iat[row-1, 3]))
plate_name = RSLNamer(df.iat[row-1, 2]).parsed_name
plates.append(dict(plate=plate_name, start_sample=df.iat[row-1, 3]))
input_dict['source_plates'] = plates
return input_dict
@@ -1373,6 +1375,16 @@ class WastewaterArtic(BasicSubmission):
# Because generate_sample_object needs the submitter_id and the artic has the "({origin well})"
# at the end, this has to be done here. No moving to sqlalchemy object :(
input_dict['submitter_id'] = re.sub(r"\s\(.+\)\s?$", "", str(input_dict['submitter_id'])).strip()
try:
input_dict['ww_processing_num'] = input_dict['sample_name_(lims)']
del input_dict['sample_name_(lims)']
except KeyError:
logger.error(f"Unable to set ww_processing_num for sample {input_dict['submitter_id']}")
try:
input_dict['ww_full_sample_id'] = input_dict['sample_name_(ww)']
del input_dict['sample_name_(ww)']
except KeyError:
logger.error(f"Unable to set ww_processing_num for sample {input_dict['submitter_id']}")
if "ENC" in input_dict['submitter_id']:
input_dict['submitter_id'] = cls.en_adapter(input_str=input_dict['submitter_id'])
return input_dict
@@ -1642,6 +1654,7 @@ class WastewaterArtic(BasicSubmission):
output.append(dicto)
# else:
# output = super().adjust_to_dict_samples(backup=False)
return output
def custom_context_events(self) -> dict:
@@ -1751,7 +1764,7 @@ class BasicSample(BaseClass):
sample['Submitter ID'] = self.submitter_id
sample['Sample Type'] = self.sample_type
if full_data:
sample['submissions'] = [item.to_sub_dict() for item in self.sample_submission_associations]
sample['submissions'] = sorted([item.to_sub_dict() for item in self.sample_submission_associations], key=itemgetter('submitted_date'))
return sample
def set_attribute(self, name:str, value):
@@ -1857,19 +1870,6 @@ class BasicSample(BaseClass):
template = env.get_template("basicsample_details.html")
return base_dict, template
def show_details(self, obj):
"""
Creates Widget for showing sample details.
Args:
obj (_type_): parent widget
"""
logger.debug("Hello from details")
from frontend.widgets.sample_details import SampleDetails
dlg = SampleDetails(parent=obj, samp=self)
if dlg.exec():
pass
@classmethod
@setup_lookup
def query(cls,
@@ -2126,6 +2126,7 @@ class SubmissionSampleAssociation(BaseClass):
sample['Well'] = None
sample['Plate Name'] = self.submission.rsl_plate_num
sample['Positive'] = False
sample['submitted_date'] = self.submission.submitted_date
return sample
def to_hitpick(self) -> dict|None: